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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MolluscDB PartiGene database Resource Report Resource Website 1+ mentions |
MolluscDB PartiGene database (RRID:SCR_006069) | MolluscDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database housing EST information from nine mollusc species, including Lymnaea stagnalis, the pond snail. Co-curated with Angus davison of Nottingham University. | lymnaea stagnalis, biomphalaria glabrata, mytilus galloprovincialis, mytilus edulis, argopecten irradians, crassostrea gigas, crassostrea virginica, dreissena polymorpha, sequence, blast, fasta, expressed sequence tag | has parent organization: nematodes.org | nlx_151475 | SCR_006069 | 2026-09-05 06:25:46 | 2 | |||||||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-09-05 06:25:46 | 89 | |||||
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HCV Sequence Database Resource Report Resource Website 10+ mentions |
HCV Sequence Database (RRID:SCR_006019) | HCV Sequence Database | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. | hepatitis c virus, sequence, annotation | has parent organization: HCV Databases | Hepatitis C | NIAID | PMID:15377502 | Public | nlx_151411 | SCR_006019 | Hepatitis C Sequence Database, Hepatitis C Virus Sequence Database, Los Alamos hepatitis C sequence database | 2026-09-05 06:25:45 | 19 | ||||
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CMHD - Centre for Modeling Human Disease Resource Report Resource Website 10+ mentions |
CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) | CMHD | analysis service resource, biomaterial manufacture, data or information resource, database, material service resource, production service resource, service resource | Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges | mutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human disease |
has parent organization: Toronto Centre for Phenogenomics is parent organization of: Centre for Modeling Human Disease Gene Trap Resource |
Human disease | CIHR ; Genome Canada |
Non-CMHD users are required to register and log in only if you wish to view images on our mouse models. | nlx_151636 | SCR_006101 | Centre for Modeling Human Disease | 2026-09-05 06:25:47 | 12 | |||||
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PRED-GPCR Resource Report Resource Website 1+ mentions |
PRED-GPCR (RRID:SCR_006196) | PRED-GPCR | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries. | g-protein coupled receptor, classification, hidden markov model, sequence, fasta, family classification, motif, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:15215415 | nlx_151741, biotools:pred-gpcr | https://bio.tools/pred-gpcr | SCR_006196 | PRED-GPCR: GPCRs Family classification from sequence alone | 2026-09-05 06:25:48 | 2 | ||||||
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Multiple Mapping Method Server Resource Report Resource Website 1+ mentions |
Multiple Mapping Method Server (RRID:SCR_018015) | MMM server | alignment software, data access protocol, data processing software, image analysis software, service resource, software application, software resource, web service | Web server for modeling protein structure by using Multiple Mapping Method. Approach to sequence-to-structure alignment in comparative protein structure modeling. | Modeling protein structure, multiple mapping method, sequence, structure, alignment, comparative protein structure | PMID:16437570 | Free, Freely available | SCR_018015 | Multiple Mapping Method server | 2026-09-05 06:28:29 | 3 | ||||||||
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MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | alignment software, data processing software, image analysis software, software application, software resource | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NIAID N01 AI15447; NLM R01 LM06845; NSF IIS 9902923 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-09-05 06:28:32 | 547 | |||||
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PROMALS3D Resource Report Resource Website 50+ mentions |
PROMALS3D (RRID:SCR_018161) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints. | Structure alignment, 3D structure, sequence, protein, amino acid, homolog identification | DOI:10.1093/nar/gkn072 | Free, Freely available | SCR_018161 | 2026-09-05 06:28:31 | 50 | ||||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | alignment software, data processing software, image analysis software, software application, software resource | Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets. | Sequence, snap file, single nucleus, ATACseq dataset, data | is used by: scATAC Pipeline | Free, Available for download, Freely available | SCR_018097 | Single Nucleus Accessibility Profile Tools, Single nucleus accessibility profile Tools | 2026-09-05 06:28:31 | 16 | ||||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/, https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal | SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-09-05 06:28:35 | 20 | ||||||
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2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation Resource Report Resource Website 1+ mentions |
2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) | 2019nCoVR | data or information resource, disease-related portal, portal, topical portal | Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data. | COVID-19, sequence, genome sequence, genome variation, data, China National Center for Bioinformation | COVID-19 | Free, Freely available | SCR_018342 | 2019 Novel Coronavirus Resource, 2019 Novel Coronavirus Resource (2019nCoVR), CNCB 2019nCoVR, CNCB 2019 Novel Coronavirus Resource | 2026-09-05 06:28:35 | 4 | ||||||||
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rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data analysis software, data processing software, software application, software resource | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-09-05 06:28:11 | 1 | |||||||||
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Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | data access protocol, data or information resource, portal, software resource, web service | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-09-05 06:28:12 | 17 | ||||||||||
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MOLE-BLAST Resource Report Resource Website 1+ mentions |
MOLE-BLAST (RRID:SCR_016644) | moleblast, Mole Blast, MOLE BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results. | taxonomist, find, close, database, submitted, query, sequence, generate, phylogenetic, tree, nucleotide | works with: NCBI BLAST | Free, Freely available | SCR_016644 | 2026-09-05 06:28:12 | 3 | |||||||||
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Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | alignment software, data access protocol, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, web service | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-09-05 06:28:13 | 0 | |||||||||
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Rampart Resource Report Resource Website 1+ mentions |
Rampart (RRID:SCR_016742) | data processing software, software application, software resource, workflow software | Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems. | workflow, management, system, de novo, genome, assembly, DNA, sequence, data, high, performance, computing, environment, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom |
BBSRC | PMID:25637556 | Free, Available for download, Freely available | biotools:rampart | http://www.earlham.ac.uk/rampart/, https://bio.tools/rampart | SCR_016742 | 2026-09-05 06:28:13 | 2 | ||||||
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Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | alignment software, data analysis software, data processing software, image analysis software, software application, software resource | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian Government ; Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-09-05 06:28:16 | 203 | ||||||
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Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | 2026-09-05 06:28:16 | 182 | |||||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | data analysis software, data processing software, software application, software resource | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIDA P30 DA018310; NIGMS R01 GM067193 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-09-05 06:28:15 | 14 | ||||||
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Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-09-05 06:28:14 | 20 |
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